Xenogenesis
by cmartist
Summary: What if Rei Ayanami wasn't just the product of Gendo's research? Is she really a clone of Lilith? What if she was more than she appeared to be? Ch. 2 finally up.
1. 01 Prologue

**Xenogenesis**

Disclaimer: Xenosaga and Neon Genesis Evangelion belong to who they belong. What? You thought this was gonna be longer?

**Prologue**

"We'll be caught in the explosion! We have to get out of here quickly!" Shion yells over the explosions rocking Proto Merkabah. One of the more powerful ones knocks her to her feet followed by a massive rumbling.

"What was that?" asks Ziggy, his cybernetic sensors picking up the increased frequency of the rumbles.

"More explosions?" MOMO looks around in fear and subconsciously latches on to her protector as the whole station starts to shake.

"No. It's faint, but it feels like we're...changing directions?" adds Chaos questioningly. Although he appeared human, the full extent of his abilities was still unknown by the people around him.

KOS-MOS, who had been silent all this time, had been busy scanning the area and finally spoke up. "Shion. I have confirmation of ignition in the Proto Merkabah's propulsion units," she says, her voice in its usual monotone. Going silent as her scanners start feeding her more data, she faces her creator as the final figures come in. "It is descending towards Second Miltia now."

The whole group looks on in shock at her statement. A station the size of Proto Merkabah striking Second Miltia would be the equivalent of the impact which destroyed ancient Earth all those millennia ago. As the station began its deadly plunge, one observer in orbit around the planet looked on in amusement and glee as images of death and destruction danced in his mind.

"Well then, let's just see how powerful you all are..."

Back on the station, Shion had finally recovered from the shock of the information, getting back on her feet and facing KOS-MOS. "Are you sure about this?" she asks.

"Yes," comes the emotionless reply. "Should its descent continue at present speed, we will enter the atmosphere in approximately 8 minutes."

"Looks like 'he' planned this," Ziggy adds, unknown to him that the person was just outside the station watching.

"That bastard!" growls Jr. "He's got too many tricks up his sleeve..."

"Based on the current angle of approach, breaking up the facility into approximately 28,000 pieces would result in 99.6 of them vaporizing before impact..."

"...if we detach each sub-component?" finishes Shion as she realizes what KOS-MOS was suggesting.

MOMO also realizes the plan and starts searching her memory for any way to implement that idea. At last she finds the data she was looking for, opening her golden eyes and facing the group. "The control room...the control room on level 33 will allow us to detach the facility!" she finishes hurriedly.

"We'd better hurry! There's no time!" Chaos adds.

The group rushes to the control room, precious seconds ticking away with each step they take. Finally finding an elevator which would lead them to the location, MOMO heads to the terminal and starts inputting commands faster than any human could into the console.

"Oh no!"

"Is there a problem," Ziggy asks gently of the little girl.

MOMO doesn't look up from the terminal as she continues to punch away at the keys. "It's bad. The entire process from system startup to complete detachment takes one whole minute! That won't give us enough time to return to the Elsa!"

"Is this the only place we can activate it from?" asks the cyborg, his face a mask of calm. "We can't do it remotely?"

MOMO shakes her head in resignation and fear. "No. The system was built so that the command will only be accepted from here."

Jr stomps his foot angrily on the metal flooring. "Damn...So the only way to stop this thing is to go down with it?"

"This can't be...There has to be another way!" Shion pleads, as if her silent wishing would come true.

"There isn't!" MOMO adds, tears threatening to fall from her eyes. "I've searched again and again, but we can only activate it from here!"

Everyone remains silent, unable to think of another solution. A voice speaks up however, shaking them out of their stupor.

"Please head back now," comes KOS-MOS firm command.

"What, KOS-MOS?" Shion looks to her android like it had suddenly grown a second head.

"Shion, please return to the Elsa with the others," KOS-MOS reiterates, her primary directive of protecting her creator coming to the forefront. "I will stay behind to initiate the detachment sequence."

"Wait a second? Stay behind? Are you joking?"

"This facility will enter the atmosphere shortly. We will exceed the tolerances for maximum temperature in three minutes and 28 seconds. Please hurry. I suggest you return to the Elsa before then." Before Shion can retort, KOS-MOS cuts her off and starts walking towards the console. "My self-preservation programming is functioning properly. I have no intention of remaining on this facility to the very end. Do not worry. At maximum speed, I can reach the Elsa in under one minute."

"You're sure?" asks Ziggy.

"Yes. This option guarantees the highest probability of success."

Seeing as that was going to be her only reply, Ziggy calls for the others to head back to the ship. Shion however, in true fashion, still refuses to abandon the android.

"Trust her, Shion. It'll be ok. She'll catch up. Now c'mon!" Jr. adds as he starts his run back. Reluctantly, she agrees and follows the rest of the group. Turning back only once to scold her uncooperative creation.

"You'd better come back, KOS-MOS!"

The group had already made its way a quarter of the way back to the ship when a new set of explosions start rocking the floor, the detachment sequence already starting. From the outside, it appeared the station was coming apart like a giant 3D jigsaw puzzle, years of missing research becoming lost with each falling part. The group finally makes it back to the Elsa, out of breath but alive.

"Matthews!" Jr. calls as he enters the bridge.

"Little Master! What's all this shaking? What the heck did you guys do?" asks the captain.

"Proto Merkabah's about to re-enter the atmosphere. If left unchecked, it'll crash into the planet..."

Matthews looks on in shock. This was definitely not what he signed up for when he agreed to work for Jr. and the Foundation.

Seeing that Matthews was still in shock, Jr. brings him up to speed with the plan KOS-MOS was currently implementing.

"We detached all the sub-compartments and that's what's causing all the shaking. Anyway, we'll get into more details later. Just prepare for immediate take-off!"

"Right, let's...What! Prepare? Why don't we leave just now?"

"KOS-MOS is still inside. We're going to wait for her!"

"But aren't we in danger if it's already detaching?"

Jr turns to the captain, the look in his eyes showing that there was no convincing him otherwise. "I'm aware of that, but if I SAY we wait, we wait!"

Looking at the control panel, KOS-MOS continues to punch away at the keys, finalizing the sequence which would complete the separation of Proto Merkabah.

100 separation initiated comes the reply from the computer.

KOS-MOS turns around and begins her run back to the Elsa. As she is running, an odd current runs through her system, causing her to stumble slightly. _'It appears there is some power imbalance in my control matrix. I will have to request Shion examine it when I return,'_ she notes to herself. Increasing her speed to compensate for the stumble, she reaches the stairwell to the Elsa only to find that it had already collapsed due to falling debris. _'Recalculating new route,'_ her internal systems reply. Sensing that the platform where the ship was docked was also destroyed, she assumes that the ship had already left the area and escaped to space. KOS-MOS begins to plan for another means of escape seeing as her ride was no longer an option. Before she can even begin to find a path, a silent voice speaks into her mind.

"See with your heart, KOS-MOS," the voice beckons.

'_I have no heart,' _she replies, unsure why she even replied to the voice.

"See with your heart," the voice repeats.

A sudden feeling comes over KOS-MOS as she looks down a corridor, a particular wall coming to mind. _'Is this what humans call...a hunch?'_ she thinks to herself. _'There is a 50 probability of survival if I attempt to take one of the fighters and escape from Proto Merkabah yet...something else is telling me to take this corridor.' _The entire debate merely took nano-seconds for KOS-MOS but finally ignoring her logic program she decides to go with the 'hunch' and run down the corridor. Traveling several hundred meters in what would have certainly wiped out a normal human, she stops at a particular point in the wall, gazing at it curiously as the 'hunch' starts acting up again.

"Maximum output," she whispers to no one in particular. Pointing her right hand at the wall, it transforms into ion cannon mode and begins charging. As it reaches full charge, KOS-MOS lets loose a wide beam of energy, neatly incinerating everything in its path. Running forward as the beam continues its destructive path, she dodges falling debris as she makes her way through the makeshift tunnel. Finally blasting through the outer wall, KOS-MOS jumps through the hole not really expecting to see anything. A small part of her thinking that this is not how she would have wanted everything to end. _'I...want?'_ she thinks. However, as she clears the smoke, the blue and white hull of the Elsa can be seen patiently waiting for her.

"KOS-MOS!" cries Shion, her hand outstretched and ready to grab her.

KOS-MOS reaches out and catches the hand, her body unfortunately too heavy for Shion to manage correctly which causes her to slam into the ship's hull. Fortunately for her, being an android had its perks and she barely felt the slam.

Shion struggles to bring KOS-MOS into the ship, the weight posing more of a problem than realized. Her arm already straining just to hang on, she feels KOS-MOS slowly slipping through her grasp. _'No! I can't hold on!'_ Just as she looses her hold on the android, a second hand grabs KOS-MOS, saving her from a fiery death. Looking to her helper, Shion is surprised to see the cyborg right behind her. "Ziggy!" she beams.

"I've got them both," he says into the ship's intercom. "Tale us out of here!"

As the ship blasts away from the collapsing Proto Merkabah, Shion collapses onto the floor in relief. Looking towards KOS-MOS, she sighs as she rubs her sore hand. "I really better start putting you on a diet," she jokes.

'_Is that what is called a 'joke'?' _she thinks. Turning to her creator, she is mildly surprised when Shion suddenly latches on to her and starts crying.

"Something's not right" says Ziggy, the ship starting to shake violently. "Let's go," he commands.

Shion dusts off her uniform and rushes to the lift. Seeing KOS-MOS starting to get to her feet as well, she follows Ziggy through the ships corridors.

As KOS-MOS follows Shion, another 'hunch' makes its way to her mind, calling her to head to the cargo bay. Debating whether to follow the Vector employee or go with the 'hunch,' KOS-MOS decides to patch in to the ship's communications network and overhears the frantic yells on the bridge.

The angle of approach is too steep! cries one voice. _'Shion's assistant.'_

Can't you fix it! yells a voice. _'Captain Matthews,'_ she thinks.

It's no good! The controls aren't responding! replies Tony.

Impossible! All the systems show green!.

The stabilizers must have been damaged by the debris! Tony adds. We can't change the angle any more than what we have!

She shuts off the comm. system, her decision already made. Walking to the cargo bay, she starts calculating all the variables needed to fulfill her prime directive...protect Shion at all costs.

What will you do? the voice asks.

chaos looks down at his hands, a feeling of helplessness washing over him as the ship continues its deadly plunge. _'Can't I do anything?'_ he cries out silently. Feeling more and more helpless with each passing second, he is shaken out of his stupor as he hears someone coming down the lift. _'Who could be coming here at this time?'_ chaos wonders. As the figure steps out of the shadows, he sees the familiar white boots and clear blue hair of the battle android heading towards the airlock. "You're...?" KOS-MOS doesn't answer him as she continues her final walk. He calls out again, hoping to find out her intentions. "What are you...?" He is interrupted when KOS-MOS finally speaks, her voice soft and somewhat...sad?

"Release your pain...onto me." Theses were the last words he heard from her as she disappears down a dark corridor, the path to the airlock.

As the doors close behind her, KOS-MOS begins charging all her systems to full power. It wasn't as if there was any other alternative. _'Is this...fear? Do I fear death?'_ Pushing that thought aside, she pushes the button before her, opening the airlock and jumping out into the fiery hell raging around the ship.

"The aft hatch is opening!" Hammer yells.

"What the hell? Are they trying to burn us from the inside!" Matthews shouts. "Who's down there?" he asks the group.

Shion looks around and sees that her android once again out of sight, a chill running up her spine as she realizes what just happened. "It can't be..."

Outside, KOS-MOS crosses her arms across her head, shielding it as best she could from the heat generated by re-entry. Heat shields at 95 capacity reports her internal sensors. Her outer skin created out of a high density compound, it showed no signs of damage from the searing fire. She knew however that she was not built to withstand such temperatures. As she maneuvers herself to the bow of the Elsa, her communicator comes online with a transmission from inside the ship.

KOS-MOS! You get back this instant. You can't survive those temperatures!

"Shion," KOS-MOS replies. "I will proceed to shield the Elsa with my energy field. Please stabilize the ship during that time."

What do you think you're doing? What will that accomplish? comes the angry retort.

"Do not worry." _'Worry. I should be worried yet I am not.'_ "Maintaining this position for one minute and 20 seconds will save the Elsa." _'Yet I know my body will not survive longer than that,'_ comes the unspoken thought.

But you'll be incinerated if you do that! Stop this at once!

'_She is my creator. She would know,'_ KOS-MOS thinks to herself. _'I couldn't return to the ship now even if I was ordered to.'_ She was too far from the hatch to be able to make it safely back anyway. Nearing the bow of the ship, she activates the communicator one last time. "I am happy...to be of service." Cutting off the signal, KOS-MOS positions herself right in front of the Elsa, now taking the brunt of the re-entry heat. Feeling parts of her armor starting to char, she stretches out her arms, spreading herself out as wide as possible to protect the ship behind her. 60 seconds to heat shield failure reports her sensors. Ignoring every warning that her body was throwing at her, she remains steadfast in her position

45 seconds Pieces of her outer armor begin burning and breaking off.

30 seconds The helmet breaks off from her head, her long blue hair now flowing freely.

10 seconds. Internal systems near meltdown.

5

4

3

2

1

_Take my pain_ comes a gentle voice. KOS-MOS eyes begin to glow blue as six snow white wings erupt from her back, growing to enormous size and covering the entire Elsa. As the wings fully envelope the ship, her systems finally give out from the tremendous heat and stress, the last thing KOS-MOS sees is a bright flash of light and then darkness.

0

"Rei, you will pilot Unit-01!" barks a monotone voice.

The girl struggles to open her eyes, red pupils staring at the lights above. _'I am...lying down,'_ she thinks to herself. She also notices that one of her eyes is currently bandaged.

"Rei! I said you will pilot Unit-01!" commands the voice a second time.

'_Rei? Is that...my name?'_ Unable to answer the question herself, she decides to follow the voice and get off the bed. As she wills her muscles to move, a sharp pain runs up her spine and courses through her whole body, causing her to cry out in both surprise and pain. _'Pain? Is this what pain is?'_ comes the thought. Before she can get out of the bed, the floor begins to shake tremendously, causing her to fall out of the bed and aggravate the pain all around her body. The next few moments are a blur for her as she hears several loud crashes around her and two hands lift her off the cold floor. The last thing she hears are the quiet whispers of 'I mustn't run away' from what sounded like a young boy before darkness overwhelms her.

To be continued in the next chapter-

Author's note:

Even I'm curious how this will turn out. We'll just have to see now won't we?


	2. 02 Awakenings

**Xenogenesis**

Disclaimer: Xenosaga and Neon Genesis Evangelion belong to who they belong. What? You thought this was gonna be longer?

mystlady - thanks to my very first reviewer. I hope I can keep this story going.

And now, on with the story.

**Awakenings**

The girl's eyes open as the suns rays filter through the curtain, her red pupils staring up at the hospital ceiling. _'An unfamiliar ceiling,'_ she thinks to herself. As she tries to sit up, she notices her arm in a cast. Raising her left arm to her face, she also discovers that her head is also bandaged. Before her curiosity can get the better of her, the hiss of the room's doors calls her attention. Turning to face her visitor, she sees a woman with blonde hair dressed in a typical doctor's gown, her glasses reflecting the light just right to hide her eyes.

"How do you feel, Rei?" the person asks.

'_Ritsuko,'_ her mind recalls. "I am operating at 67 capacity," she replies, causing the blonde doctor to raise an eyebrow in curiosity. "May I ask how long I was incapacitated?"

"You've been asleep for 3 days," comes the reply. "By my estimates you'll be healed within 20 days. You will resume piloting Unit-00 at that time."

"Affirmative. What are my directives until then?"

'_Rei is acting a bit strange,_'Ritsuko thinks before putting it off as something Rei would say. "Just do what you normally do," she answers before leaving the pale girl alone in the room.

Said girl simply stares at the door where the doctor left before turning her gaze back to the ceiling. "Accepted," she says before closing her eyes once more.

* * *

"Rei, it's time for you to go to school," the doctor says as she gently wakes the sleeping albino.

"Hai," she softly replies. Fighting the pain that shoots up her body as she gets to her feet, she notices a school uniform lying on the chair beside the bed. She takes a look at the clothes then back at the doctor. Staring for a few moments, she looks back at the school uniform as Ritsuko finally gets the idea.

"Oh...I'll let you get dressed, then," she blushes in reply. She then steps out of the room, leaving Rei with the school uniform. _'That was unusual. Rei never showed any signs of modesty before. Perhaps something to do with the accident,'_ she muses to herself as she walks back to her office.

Rei watches in mild curiosity as she watches the doctor leave the room. Shuffling towards the clothes, she picks up a white pair of panties and stares at it intently before suddenly remembering how to put them on. Careful to avoid injuring her already damaged arm, she finally gets the school uniform on after several failed attempts. Giving herself a once over to make sure everything is in it's proper place, Rei walks out the sterile room and heads off to school.

* * *

Shinji shuffles nervously as he enters his new classroom. Many types could be seen in the relatively ordinary setting; the jocks, the nerds, girls, boys, simply a great melting pot of people. _'People who will only hurt me in the end,'_ he thinks bitterly to himself. Taking a spot in a vacant seat, his eyes roam around the room, finally falling on the first child, Ayanami. Looking over her, he notices all the bandages covering her lithe body, her head and arm the most noticeable of the injuries _'Eh? Did she get those before I chose to pilot?'_ he wonders. Sighing his typical sad sigh, he prepares for his first day of school when he overhears some students behind him talking.

"Do you think he was injured?" asks a male student, piquing Shinji's interest.

"What? In that robot incident! The television said no one was injured!" a girl replies

Shinji cringes in worry. _'Was someone hurt while I was fighting?'_

"No way!" retorts the boy. "Didn't you see the explosion on Mount Takanasou? There were planes and soldiers everywhere. I'll bet ten or twenty people were injured, and I'm pretty sure some were killed as well," he adds.

Unable to take any more, Shinji puts on his SDAT player and drowns out the sounds of reality.

"You don't have to sound so happy about it!" the girl cries. Her reply is cut short as a student enters the classroom, a huge scowl on his face. "Suzuhara," she calls.

"Wow, has the class population dropped or what?" he comments sarcastically.

"They've all either transferred or evacuated, Touji. No one in their right mind would stay in this city after that last attack."

"Oh, does that explain why you're here?" Touji smirks.

"Yup," he cheerfully replies. "Speaking of which, what happened to you? We thought you got drafted or something and got involved."

"My sister did," he answers bitterly. "She got crushed under a pile of debris that _robot_ caused!" Touji angrily recollects. "She's in the hospital now but since both my dad and grand-pa are in the lab, they can't get out to visit her. I'm the only one she has right now." His hands clench tightly at the memory, his knuckles turning white. "If I ever get my hands on that dumb pilot who did this, I'm gonna beat him up! What the hell did he think he was doing! Wrecking our own city!"

The kid in glasses looks up in thought for a moment before turning back to Touji. "Hmm, I dunno what he was thinking. Btw," he begins to whisper. "Have you heard the rumor about the new transfer student?" he asks, pointing to the living catatonic known as Shinji.

As the two begin coming up with theories about the new student, they fail to notice two red eyes watching them intently. The silent observation stops though as the teacher finally makes his presence known.

"Class! Rise!" barks the girl from earlier as she commands the class to welcome the teacher. The students stand up briefly then sit once again, the teacher having taken his spot at the front of the class. With the introductions done, the teacher begins his lecture on history, failing to realize this was a math class.

"...and so the earth was thrown off its axis as the..." drones the teacher.

Rei looks forward intently for once, gaining some stares from her classmates as the pale girl never showed any attention in class. Their curiosity disappears however, as she resumes staring outside the window, disinterested once more with life. In reality however, Rei's mind was far from inactive in those brief moments that she was paying attention to class.

'_The lesson that the teacher was explaining...it is wrong,'_ she thinks to herself. _'Those were not the events that caused Second Impact.'_ Her musings are interrupted as the class bursts into chaos, all of the students collecting around Shinji with questions flying all around.

"You're a pilot!" "That's so cool! Wanna hang out?" "That guy's the pilot?"

Even with all the noise in the room, the teacher still continues on with his ramblings until the sound of the bell is heard. "Oh? Is it time already? You may go now," he mumbles.

Shinji continues to fumble around answers to the barrage of questions before him, oblivious to the glare a certain student was giving him. As the class begins to disperse, Rei's gaze follows Shinji as he makes his way out of the classroom.

* * *

Shinji falls to the dirt as a fist slams into his face, the owner of the fist glaring at him in anger.

"Sorry, newcomer, but I've got to beat you up," he growls. "I've got a lot of anger to work off." Having done his part, Touji turns and walks away, not quite satisfied but feeling somewhat sorry for the wimp before him. _'If he's the kind of people they put in the pilot seat, no wonder my sister got hurt,'_ he growls silently.

Shinji looks up at his attacker, his anger rising for the first time in ages, before being squashed back by his own cowardice.

"Sorry 'bout this," the boy in glasses responds. "His sister was injured during that fight, or at least that's what he says is his excuse anyway."

"I didn't pilot it by choice," Shinji retorts softly but loud enough for Touji to hear.

'_That punk! I let him off with just one punch and he tries to make excuses for hurting my sister!'_ Turning back to face Shinji, he picks up the small boy by his collar and glares angrily at him, taunting the boy to fight back. His irritation increases as Shinji merely looks indifferent. _'Take me lightly, will ya!'_ Drawing back his fist for another blow, he lets lose another punch but feels his wrist caught by a vice-like grip.

"You will release pilot Ikari," comes a cool emotionless voice.

Turning to the source of the voice, he sees the pale Ayanami preventing his fist from connecting with the boy before him. "Shut up! You don't know what this guy did!" he yells back as he tries to break free of the hold. His anger partly turns to shock as he finds that he cannot get out of the smaller girl's hand.

"If pilot Ikari had not agreed to pilot Unit-01, there would have been a 98 chance that NERV would lose the battle and a 100 chance your sister would cease to exist," she replies, her eyes never leaving Suzuhara's own.

Touji tries to glare back at the albino but the way she was staring at him simply unnerved the larger teen. "What's it to you!" he yells, trying to regain his courage. "Why are you standing up for this guy!"

"My injuries prevented me from piloting, thus pilot Ikari was required to take the role," she replies emotionlessly. "By your reasoning, it was through my inaction that your sister was injured. Do you wish to confront me as well?" she asks, squeezing the boy's wrist slightly.

Fighting the shaking in his knees, he tries to recover the last of his pride by giving an arrogant sniff. "Che." Touji yanks his hand out of Rei's grip, a light bruise forming where the girl held him. "You're lucky I don't fight girls," he weakly retorts.

Rei looks on impassively at the boy in front of her. "Had you accommodated my request earlier, we would have saved 2 minutes and 37 seconds."

Saving what remained of his pride, Touji walks away from the two teens, muttering obscenities about gorilla tomboy's and weird chicks. His friend, still in shock over Touji's 'loss' against none other than Ayanami (and the fact she was a pilot as well) stares in surprise before recovering his senses and chasing after his friend.

"He…hey! Wait up!" cries the boy with glasses.

Rei watches impassively as the two run off into the distance before turning her gaze to the fallen Shinji. "Are you injured, pilot Ikari?"

Shinji remains in his place, curled up in a fetal position. "Why did you help me?" he whispers, his head buried between his knees.

"You were in need of assistance," comes the short reply. Before Shinji can respond to that statement, a loud siren begins to sound throughout the entire city. Rei looks towards the source of the sound, her eyes narrowing slightly as her training begins to kick in. "I am going ahead to NERV. Please follow as soon as possible," she urges before running off.

Picking himself off the ground, Shinji pats the dust off his clothes as best he can before turning towards the direction Rei ran off to. "Thank you," he whispers, before heading towards NERV as well.

* * *

"Man, can you believe it! Ayanami's got one hell of a grip," Touji gripes, rubbing his sore wrist as he and Kensuke wait in the shelter.

"You're surprised? I'M surprised. I can't believe that Ayanami's a pilot. I mean, she's just...Ayanami," Kensuke answers as he tries to get a signal on his mini-TV. "They're still blocking it."

"Blocking what?" Touji asks.

"The battle, of course!" replies Kensuke as if it was the most obvious answer in the world. "Man, I wish I could be out there watching it," he moans.

"Are you stupid? Do you wanna get killed? There's gonna be a battle out there soon."

"So?" retorts the spectacled teen. "It's not like we're that much safer in here. Besides, after beating up that new kid, I wouldn't be surprised if he didn't want to pilot anymore," he comments, causing his friend to flinch in guilt.

"He...hey. He wouldn't do that. We'd all die if he didn't, right?" Touji replies, more for himself than for anything else.

"Who knows? All I know is I want to see that giant robot thing the new kid was talking about before I die. Just once, you know?" Kensuke begins fiddling with his camera for a few moments before nudging Touji. "Hey, join me in the washroom," he whispers.

"Why the heck should I join you!" he whispers back, not quite understanding the reason behind the request. After several pleadings by his friend, Touji finally relents and agrees to head to the washroom. "Hey, class rep! Me and Kensuke are headed to the washroom." _'I feel like a girl,'_(1) Touji thinks to himself.

"You were supposed to 'go' before we arrived at the shelter!" snaps someone . "Fine. Just be quick about it!" she sighs, knowing that Touji would pester her till he went (which would probably last till the alert ended).

"Thanks, Hikari. Yer the best!" he replies, giving her a roughish smile before heading out with Kensuke.

"Baka," she whispers, failing to hide the blush that now permeated her cheeks.

* * *

"So what did you want to talk about?" Touji asks.

"I'm going out to tape the battle," Kensuke replies.

"Like I said earlier...ARE YOU NUTS? DO YOU WANNA DIE SO BADLY!"

"It's not that. It's just that if the new kid doesn't fight, we're gonna all die anyway and I want to see that giant robot before then." Touji looks like he is about to reply but Kensuke cuts him off with a smirk. "Besides, if he doesn't pilot it'll be your fault. You have an obligation to watch him fight."

Touji sighs in defeat as he throws up his hands in frustration. "ARGH! Once you get an idea in your head, you just can't let it go, can you?"

"Nope. Let's open the gate, then."

Several moments later saw the two teens running up the stairs of a shrine at the top of a mountain, the school gate easily moved by Touji.

"Hey Kensuke! Why the heck do we have to run up here?" Touji pants, surprised at the endurance of the military otaku before him.

"To get a better view of course," he replies as if it was the most obvious thing in the world. Kensuke almost forgets about Touji as he sees the Angel flying in the distance. "There it is!" he nearly yells, training his hand held camera on the city.

* * *

The Angel had lazily floated into the city, ignoring all attempts by the military to attack it. Landing on the streets of Tokyo-3, the two stubs on its side suddenly sprouted long tentacles of energy, making it look even more squid-like than earlier. Off to the side, one of the tall buildings opened up to reveal Unit-01 poised and ready to strike. If only the same thing could be said about the pilot.

Inside, Shinji kept repeating the instructions Ritsuko said about firing the rifle like a mantra. "Aim the target in the center and switch..."

"-Develop the AT-field. Follow the plan, all right?-" comes Misato's voice over the comm. system.

"Hai," comes the listless reply. Jumping out of the hanger, he twirls the EVA around and empties the rifle's contents at the angel, screaming out of fear and frustration as he does so.

"BAKA! You're giving the enemy a smoke screen!" Misato yells from her post at the command center.

Rei, who was currently beside Commander Ikari was watching the battle with her usual impassiveness. A flicker of emotion can be seen in her eyes as the Angel retaliates from the smoke, cutting the rifle.

"Damn it! Send Shinji a reserve rifle," Misato orders. "Did you hear that Shinji? You should see it to your left!"

Shinji, still shaking with fear over how easy the weapon was destroyed, was in no condition to hear the orders much less fight. Shaking with fear, he barely avoids the Angel's strike as it slashes the area where he stood. The EVA, however, did not escape unscathed as a timer starts to flash on both Shinji's console and in the command center.

"Umbilical cable cut!" Shigeru reports, followed by Maya's frantic cry.

"4 minutes and 53 seconds remaining in internal battery!"

Gendo continued to watch the battle as it unfolded, unaware that Rei was no longer beside him. If he bothered to pay attention, he would have noticed her enter the elevators which headed towards the sealed area of the hanger bay.

Rei enters the sealed hanger, walking around the hardened bakelite towards her objective. Approaching Unit-0, she pauses for a moment, as if deep in thought before placing a hand on the bakelite.

* * *

Touji and Kensuke look on in fear and awe as the EVA struggles against the feelers of the Angel. "Why doesn't he fight back!" Touji shouts to Kensuke, the two rooted to the spot as their legs refused to work.

"Is it because...we're here?" Kensuke wonders out loud. "He's trying to protect us!"

Back at the command center, people were getting more and more frantic as the EVA's remaining power continued to dwindle. "3 minutes and 28 seconds remaining!" reports Maya as Misato contemplates what to do with the 2 civilians outside the EVA.

"Shinji! Let them into your cockpit. After you get them, retreat and we'll confront the Angel later!"

Ritsuko, who had been silent for most of the battle, finally speaks up with Misato's order. "We can't allow civilians into the entry plug," she warns.

"I'll allow it for now," Misato counters, her personality now very unlike her off-duty one.

"You're exceeding your authority 'Captain' Katsuragi," Ritsuko adds.

"Maya, open the EVA's external speakers!" Ignoring Ritsuko's warnings, and ordering the two teens into the entry plug. Ritsuko frowns however, as the screen begins to show problems with the EVA.

"Those two are interfering with the nervous system. Noise is getting generated in the nervous pulses."

"Shinji! Retreat now!" Misato commands. Unfortunately, NERV's alarms begin blaring as something else begins to make itself known. "What is it now!" Misato asks.

Maya rushes to check her console and her eyes widen in shock as she reads the data. "I...impossible...it can't be," she stutters.

"Out with it already!" Ritsuko snaps impatiently as she heads over to Maya. Looking at the data, even she pales at what she sees.

"Well? What is it?" Misato asks. Her question is cut short as Rei's voice suddenly comes through the speaker systems.

"-Captain Katsuragi, I require launch bay 12 to activate,-" comes the cool emotionless voice.

"Rei? What the? Why do you need launch bay 12?"

"Because she's in Unit-0," comes Ritsuko's shaky reply.

Even Gendo's normally cool front crumbles as he stands up from his seat in shock. _'Impossible. Unit-0 was frozen in bakelite. It would take days to remove it. And even so, Unit-0 has no power whatsoever. It shouldn't even be moving.'_ Gendo thinks to himself, too much in shock to even bark out an order. _'What the hell is going on?'_

"-Captain Katsuragi. I require launch bay 12 to activate. Pilot Ikari is in danger,-" Rei repeats.

Hearing about Shinji shakes Misato out of her shock as she orders Maya to launch the EVA.

"You only have 48 seconds of power!" Ritsuko warns as she takes a look at the EVA's readings. "It will take you 10 seconds just to reach the surface!"

"-That is more than sufficient,-" comes the cool reply.

"Launching EVA!" Maya calls out as the launch bay activates, propelling the yellow humanoid weapon to the surface.

"C'mon, transfer student! We gotta move!" Touji yells as the Angel's feelers burn against the EVA's hands. The problem was however much Shinji wished to move, the EVA simply couldn't understand his commands with all the interference from the two extra passengers.

'_I mustn't run away, I mustn't run away,'_ Shinji chants to himself as the power meter notes less than a minute of power left. His chanting is broken however as Rei's face suddenly appears on the monitor.

"-Pilot Ikari, activate your progressive knife. I will signal you when to strike,-" orders Rei, her voice cool and controlled.

Hearing her speak without any fear gives Shinji a much needed boost of courage as he nods his head and activates the weapon system.

Rei looks at the timer before her as her EVA continues its trip to the surface. _'41 seconds.'_ As the counter hits 34, the bay hits the surface, catapulting Unit-0 into the sky. Intentionally not attaching the restraining bolts, Rei had planned to use the inertia of the launch to send her at the Angel. Landing right behind her target, she grabs each of the offending tendrils, ignoring the burning sensation in her hands as the pain is transmitted through the EVA. _'30 seconds.'_ "Now!" she calls to Shinji.

Hearing Rei, Shinji jumps into action. Drawing the progressive knife from its bay, he charges at the Angel while letting out a tortured cry. Stabbing the Angel in its core, the knife begins throwing sparks as it begins to tear into the Angel.

"UAAAaaaahhhhh!" Shinji yells as he continues to push the knife in deeper.

Back at the command center, Maya continues to monitor the power status of the two Evangelion units. "Unit one and zero. Active time is 10, 9 8, 7, 6, 5, 4, 3, 2, 1." Upon reaching '0', both EVAs cease to move, their cells completely drained. In what seemed like an eternity, the entire bridge crew held their breath before Makoto broke the silence with his statement.

"Target is completely silent."

Everyone lets out a sigh of relief as the Angel finally stops moving, its core turning a dull red color. Gendo's thoughts however were in turmoil over two things: Unit-0 getting out and the fact it was Rei who had done it. _'The scrolls did not foresee this,'_ he worries. Giving Ritsuko a silent signal, the two head out to meet Rei, both determined to find out how it happened.

Unaware of what the two had planned for her, Rei calmly waited in the seat of the entry plug, herself curious as to why she had gone out to rescue Shinji. _'Shinji...Shinji was calling,' _she remembers herself thinking.

'_It is against protocol to simply take the EVA without authorization,' _she thinks before another thought comes to mind. _'But it was the right thing to do.'_ Several more thoughts would pass through Rei's mind before the entry plug was finally opened. If anyone had been with her during that time, they would have seen Rei's eyes flickering between red and blue.

* * *

To be continued. 


End file.
